tbuckley/cabot-search huggingface dataset:
DIPG-14. PROTEOGENOMICS PROFILING REVEALS ENRICHED NON-HISTONE PROTEIN METHYLTRANSFERASES AS NEW THERAPEUTIC TARGETS IN DIPG
Authors: Arun Kumaran Anguraj Vadivel, Sanja Pajovic, Palak Patel, Robert Siddaway, Sabrina Zhu, Lauren Phillips, Cynthia Hawkins
Journal: Neuro-Oncology (2023)

Abstract Diffuse intrinsic pontine glioma (DIPG) is a devastating brain tumour arising in the brainstems of children. Despite advances in genomics and treatments, the survival rate remains zero, with a median of less than a year, making it the leading cause of death among children with brain tumours. A mutation in histone H3 protein (H3K27M) has been identified as a genetic initiation event and affects global K27 trimethylation on histone H3 proteins and DNA methylation in DIPG. The epigenetic changes caused by the H3K27M mutation suggest the existence of an H3K27M-specific transcriptome and proteome. To deepen our knowledge of DIPG, we conducted a proteogenomic analysis of DIPG tissues by using high-resolution mass spectrometry for comprehensive proteome profiling, including total proteome, phosphoproteome, and methylproteome. Integrating proteomics data with DNA methylation and transcriptomics (bulk RNAseq and single-cell RNAseq) provided new insights into DIPG tumorigenesis. Our multi-omics analyses reveal enriched translation machinery, negative regulation of apoptosis process, and non-histone protein methyltransferase proteins, suggesting their previously unknown roles in DIPG cell growth and survival. Furthermore, our findings indicate that DIPG tissues have lower global mean protein phosphorylation and higher global mean protein methylation compared to normal brains, implying that DIPG may use methyl-signaling rather than phospho-signaling for tumour growth. The translation elongation proteins EEF1A1 and EEF1A2 are the most highly methylated proteins in DIPG. Methylation modifications such as K55me2, K79me3, and K165me2 of EEF1A1 are significantly higher in DIPG tissues compared to normal brains. These enriched methylpeptides are substrates of the non-histone methyltransferases METTL13 and METTL21B, which are enriched in the multi-omics analysis. Knocking down these methyltransferases in DIPG cells significantly decreases their target protein methylation, reduces global protein synthesis, and inhibits cell growth in vitro. Thus, proteogenomic analysis of DIPG reveals tumour-enriched non-histone methyltransferases, METTL13 and METTL21B as new therapeutic targets.
BIOL-09. PROTEOMIC ANALYSES REVEAL THAT CO-CULTURE OF DIFFUSE INTRINSIC PONTINE GLIOME (DIPG) WITH CORTICAL ORGANOIDS ALTERS CELL ADHESION, DNA SYNTHESIS AND REPLICATION, AND DENDRITIC GROWTH SIGNALLING
Authors: Victoria Prior, Simon Maksour, Sara Miellet, Amy Hulme, Mehdi Mirzaei, Yunqi Wu, Mirella Dottori, Geraldine O’Neill
Journal: Neuro-Oncology (2023)

Abstract Diffuse Intrinsic Pontine Gliomas (DIPGs) are deadly brain cancers in children for which there is currently no effective treatment. In part, this can be attributed to preclinical models that lack essential elements of the in vivo tissue environment, resulting in treatments that appear promising preclinically, but fail to result in effective cures. Recently developed co-culture models combining stem cell-derived brain organoids with brain cancer cells provide tissue dimensionality and a human-relevant tissue-like microenvironment. As these models are technically challenging and time consuming it is imperative to establish whether interaction with the organoid influences DIPG biology and thus warrants their use. To address this question, we cultured DIPG cells with GFP-expressing cortical organoids. We created “mosaic” co-cultures enriched for tumour cell-neuronal cell interactions, where disaggregated spheroids and organoids were mixed and allowed to reform, versus “assembloid” co-cultures enriched for tumour cell-tumour cell interactions, where preformed tumour spheroids and organoids were combined. Sequential window acquisition of all theoretical mass spectra (SWATH-MS) was used to analyse the proteomes of DIPG fractions isolated by flow-assisted cell sorting. Control proteomes from DIPG spheroids were compared with DIPG cells isolated from mosaic and assembloid co-cultures. This revealed that tumour cell adhesion was reduced, and DNA synthesis and replication were increased, in DIPG cells under either co-culture condition. By contrast, the mosaic co-culture was alone associated with pathways implicated in dendrite growth. We propose that co-culture with brain organoids is a valuable tool to parse the contribution of the brain microenvironment to DIPG tumour biology.
IMG-05. A MULTI-INSTITUTIONAL AND MULTI-HISTOLOGY PEDIATRIC-SPECIFIC BRAIN TUMOR SUBREGION SEGMENTATION TOOL: FACILITATING RAPNO-BASED ASSESSMENT OF TREATMENT RESPONSE
Authors: Anahita Fathi Kazerooni, Nastaran Khalili, Debanjan Haldar, Karthik Viswanathan, Ariana Familiar, Sina Bagheri, Hannah Anderson, Sherjeel Arif, Rachel Madhogarhia, Meen Chul Kim, Aria Mahtabfar, Phillip B Storm, Adam Resnick, Jeffrey B Ware, Christos Davatzikos, Arastoo Vossough, Ali Nabavizadeh
Journal: Neuro-Oncology (2023)

Abstract Current response assessment in pediatric brain tumors (PBTs), as recommended by the Response Assessment in Pediatric Neuro-Oncology (RAPNO) working group, relies on 2D measurements of changes in tumor size. However, there is growing evidence of underestimation of tumor size in PBTs using 2D compared to volumetric (3D) measurement approach. Accordingly, automated methods that reduce manual burden and intra- and inter-rater variability in segmenting tumor subregions and volumetric evaluations are warranted to facilitate tumor response assessment of PBTs. We have developed a fully automatic deep learning (DL) model using the nnUNet architecture on a large cohort of multi-institutional and multi-histology PBTs. The model was trained on widely available standard multiparametric MRI sequences (T1-pre, T1-post, T2, T2-FLAIR) for segmentation of the whole tumor and RAPNO-recommended subregions, including enhancing tumor (ET), non-enhancing tumor (NET), cystic components (CC), and peritumoral edema (ED). As a prerequisite step for accurate tumor segmentation, we also generated another DL model based on DeepMedic for brain extraction from mpMRIs. The models were trained on an institutional cohort of 151 subjects and independently tested on 64 subjects from the internal and 29 patients from external institutions. The trained models showed excellent performance with median Dice scores of 0.98±0.02/0.97±0.02 for brain tissue segmentation, 0.92±0.08/0.90±0.17 for whole tumor segmentation, 0.76±0.31/0.87±0.29 for ET subregion, and 0.82±0.15/0.80±0.28 for segmentation of non-enhancing components (combination of NET, CC, and ED) in internal/external test sets, respectively. The automated segmentation demonstrated strong agreement with expert segmentations in volumetric measurement of tumor components, with Pearson’s correlation coefficients of 0.97, 0.97, 0.99, and 0.79 (p&amp;lt;0.0001) for ET, NET, CC, and ED regions, respectively. Our proposed multi-institutional and multi-histology automated segmentation method has the potential to aid clinical neuro-oncology practice by providing reliable and reproducible volumetric measurements for treatment response assessment.
The GPCR–Gαs–PKA signaling axis promotes T cell dysfunction and cancer immunotherapy failure
Authors: Victoria H. Wu, Bryan S. Yung, Farhoud Faraji, Robert Saddawi-Konefka, Zhiyong Wang, Alexander T. Wenzel, Miranda J. Song, Meghana S. Pagadala, Lauren M. Clubb, Joshua Chiou, Sanju Sinha, Marin Matic, Francesco Raimondi, Thomas S. Hoang, Rebecca Berdeaux, Dario A. A. Vignali, Ramiro Iglesias-Bartolome, Hannah Carter, Eytan Ruppin, Jill P. Mesirov, J. Silvio Gutkind
Journal: Nature Immunology (2023)
Reduction-responsive nucleic acid nanocarrier-mediated miR-22 inhibition of PI3K/AKT pathway for the treatment of patient-derived tumor xenograft osteosarcoma
Authors: Dafu Chen, Chengyue Lei, Weifeng Liu, Meiyu Shao, Meizhou Sun, Jianxun Guo, Jingjing Cao, Jing-Jun Nie, Peng Luo, Yuwen Luo, Bingran Yu, Renxian Wang, Shun Duan, Fu-Jian Xu
Journal: Bioactive Materials (2023)

miRNAs are important regulators of gene expression and play key roles in the development of cancer, including osteosarcoma. During the development of osteosarcoma, the expression of miR-22 is significantly downregulated, making miR-22 as a promising therapeutic target against osteosarcoma. To design and fabricate efficient delivery carriers of miR-22 into osteosarcoma cells, a hydroxyl-rich reduction-responsive cationic polymeric nanoparticle, TGIC-CA (TC), was developed in this work, which also enhanced the therapeutic effects of Volasertib on osteosarcoma. TC was prepared by the ring-opening reaction between amino and epoxy groups by one-pot method, which had the good complexing ability with nucleic acids, reduction-responsive degradability and gene transfection performance. TC/miR-22 combined with volasertib could inhibit proliferation, migration and promote apoptosis of osteosarcoma cells
DIPG-21. LINKING DETERMINATION OF CELL FATE IN THE DEVELOPING CENTRAL NERVOUS SYSTEM TO DIFFUSE MIDLINE GLIOMA
Authors: Liam Furst, Enola Roussel, Ryan Leung, Ankita George, Ron Firestein, Maree Faux, David Eisenstat
Journal: Neuro-Oncology (2023)

Abstract Diffuse midline glioma, K27-altered (DMG) is a treatment resistant, uniformly fatal cancer that arises predominantly in children. Next-generation sequencing has revealed that the majority of patients with DMG harbor K27M mutations in canonical histone variants H3.1 and H3.3, leading to global epigenetic dysregulation and an oligodendrocyte precursor cell (OPC) transcriptional profile. DLX2 is a homeobox transcription factor that directly represses OPC cell fate and promotes a GABAergic interneuron cell fate during neurogenesis. We identified DLX2 occupancy of early (Olig2, Nkx2.2) and late (Myt1, Plp1) genes required in OPC differentiation in vivo. Co-expression of DLX2 to target sequences reduced reporter gene expression in vitro. The Dlx1/Dlx2 double knockout (DKO) mouse showed increases in Olig2, Nkx2.2, and Plp-1 expression in vivo. Transient over-expression of a Dlx2-GFP construct into murine DMG cells resulted in significant increased expression of Gad1/2 isoforms and decreased Olig2 and Nkx2.2, global restoration of H3K27me3, as well as a reduction in migration, invasion, and colony formation in vitro. An RNAseq database containing 45 human DMG cell lines showed an inverse correlation between DLX2 expression and OLIG1/2. Cell fate changes in DLX2high/OLIG1/2low cell lines were evaluated by knockout of DLX2 using CRISPR/Cas9. Concurrently, OLIG1/2high/DLX2low expressing cell lines underwent stable transfection of an DLX2-mCherry overexpression construct. Successful alteration of DLX2 expression was confirmed by qPCR and immunoblot in knockout and overexpressing human DMG cell lines. Analysis of histone H3 marks (K27me3, K27ac), K27M, and OPC signature genes will be presented along with comparison of altered OPC genes from the Dlx1/Dlx2 DKO mouse as determined by RNAseq. The manipulation of DLX2 expression in human DMG cells both in vitro and in vivo provides a model system for assessing the contribution of a homeobox transcription factor required for neurogenesis to cell fate regulation and effects on tumorigenicity in DMG.
MDB-31. PRELIMINARY STUDY ON BIOLOGICAL SIGNIFICANCE OF WTX G435D MUTATION IN MEDULLOBLASTOMA
Authors: Yuanjun Hu, Jing Wang, Zhongping Chen
Journal: Neuro-Oncology (2023)

Abstract BACKGROUND: Previously, we reported a case of familial medulloblastoma without hereditary tumor syndrome. Through analysis of the whole genome sequencing of the family members, we found a common germline WTX (c.1863C&amp;gt;T, p.Gly435Asp) mutation in this family: cytosine (C) at position 63411863 on X chromosome was replaced by thymine (T), and the corresponding amino acid was glycine Gly (G) at position 435, which was converted to aspartic acid Asp (D). We conduct this study to explore the biological significance of this mutation in medulloblastoma cell lines. METHODS: Medulloblastoma cells (cell lines and primary cells) with stable WTX (c.1863C &amp;gt; T) hybrid mutation were contstrcuted by lentivirus transfection. The effects of WTXG435D on proliferation, invasion and chemosensitivity of medulloblastoma cells were investigated in vitro and in vivo. RESULTS: Proliferation and invasion ability of WTXG435D medulloblastoma cell were significantly weaker than WTX WT cells, and they were more sensitive to radiation and chemotherapy(cisplatin, vincristine) treatment in vitro. In vivo, animal experiments also showed that intracranial in situ tumors formed by WTXG435D medulloblastoma cells were more sensitive to radiotherapy and chemotherapy than in situ tumors formed by WTXWT ones, and the survival was longer. CONCLUSION: WTX (c.1863C&amp;gt;T, p. Gly435Asp) mutation could reduce the proliferation and invasion ability of medulloblastoma cells, and enhance the sensitivity of radiotherapy and chemotherapy. Which could be a potential therapeutic target for further investigation.
MDB-14. MULTI-OMICS OF HUMAN MEDULLOBLASTOMAS AND GENETIC LINEAGE TRACING IN VIVO IDENTIFY REGULATORS OF STEM-CELL MAINTENANCE
Authors: Bohyeon Yu, Jangham Jung, Owen Hoare, Karin Shamardani, Aaron Diaz
Journal: Neuro-Oncology (2023)

Abstract Recent studies implicate the glutamatergic lineage of the rhombic lip (RL) as the origin of group 3/4 medulloblastomas (MBs). MB stem cells resemble stalled RL progenitors and targeting common pluripotency factors induces differentiated phenotypes. However, the genetic and epigenetic regulators of stemness in MB remain incompletely understood. We profiled tissues resected from 38 patients who underwent surgery for MB at UCSF via single-nucleus RNA sequencing (snRNA-seq). Of these, 13 were also subjected to single-cell assay for transposase-accessible chromatin by sequencing (scATAC-seq). These assays generated 560,509 and 71,276 cells respectively, after quality control. Motif and latent-space analyses were used to infer cell-type specific transcription-factor expression and binding, and associated cis-regulatory enhancers. Further, we performed single-cell genetic lineage tracing on xenografts obtained from two distinct group-3/4 patient-derived lines, engineered to express heritable barcodes. We trained a machine-learning classifier on public snRNA-seq of human RL and classified Nestin-high quiescent stem-like cells, Nestin-moderate/ASPM-high proliferating progenitor cells, and glutamatergic lineage cells at various stages of differentiation in our MB clinical specimens and xenografts. Integrated analysis of these datasets maps the transition from quiescent to proliferating stem-like MB cells to more differentiated cell types at the level of transcription-factor activity and binding. We found that both the expression and binding of epigenetic regulators SUZ12, EZH2, DNMT1, and BRD7/8 were high in stem cells, but attenuated during lineage commitment. This was also the case for genes known to maintain neural stem cells in the developing brain, e.g. LIN28, FOXO3, HES6, LHX1/2/4, NUP98. Comparative analysis of developmental and MB gene expression, with motif analysis, implicates a conserved embryonal mechanism for indefinite replicative division in MB stem-like cells. These studies provide a single-cell atlas of transcriptomic and epigenetic cellular states in human MB, a map of MB cellular hierarchical organization and transcription-factor regulation of stem-cell maintenance in vivo.
Cover Image, Volume 43, Issue 6
Authors: Kayoko Hosaka, Chenchen Wang, Shiyue Zhang, Xue Lv, Takahiro Seki, Yin Zhang, Xu Jing, Jieyu Wu, Qiqiao Du, Xingkang He, Yulong Fan, Xuan Li, Makoto Kondo, Masahito Yoshihara, Hong Qian, Lihong Shi, Ping Zhu, Yuanfu Xu, Yunlong Yang, Tao Cheng, Yihai Cao
Journal: Cancer Communications (2023)

The cover image is based on the Original Article Perivascular localized cells commit erythropoiesis in PDGF-B-expressing solid tumors by Kayoko Hosaka et al., https://doi.org/10.1002/cac2.12423.
Itaconic acid underpins hepatocyte lipid metabolism in non-alcoholic fatty liver disease in male mice
Authors: Jonathan M. Weiss, Erika M. Palmieri, Marieli Gonzalez-Cotto, Ian A. Bettencourt, Emily L. Megill, Nathaniel W. Snyder, Daniel W. McVicar
Journal: Nature Metabolism (2023)

Abstract Itaconate, the product of the decarboxylation of cis -aconitate, regulates numerous biological processes. We and others have revealed itaconate as a regulator of fatty acid β-oxidation, generation of mitochondrial reactive oxygen species and the metabolic interplay between resident macrophages and tumors. In the present study, we show that itaconic acid is upregulated in human non-alcoholic steatohepatitis and a mouse model of non-alcoholic fatty liver disease. Male mice deficient in the gene responsible for itaconate production (immunoresponsive gene (Irg)-1) have exacerbated lipid accumulation in the liver, glucose and insulin intolerance and mesenteric fat deposition. Treatment of mice with the itaconate derivative, 4-octyl itaconate, reverses dyslipidemia associated with high-fat diet feeding. Mechanistically, itaconate treatment of primary hepatocytes reduces lipid accumulation and increases their oxidative phosphorylation in a manner dependent upon fatty acid oxidation. We propose a model whereby macrophage-derived itaconate acts in trans upon hepatocytes to modulate the liver’s ability to metabolize fatty acids.
IMG-09. DETERMINING OPTIMAL IMAGING SCHEDULE FOR PLGG AND PHGG PATIENTS OFF-THERAPY
Authors: Krupesh Patel, Maua Moshe, Ernest Amankwah, Leah Holloway, Stacie Stapleton
Journal: Neuro-Oncology (2023)

Abstract To this point there is no standard imaging schedule across all institutions in the surveillance of pediatric low-grade gliomas (pLGG) and pediatric high-grade gliomas (pHGG) after therapy completion. We at our institution use the Children’s Oncology Group (COG) protocols ACNS1831/ACNS1833 to guide our surveillance of pLGG. The MRI schedule is every 3 months for year 1 (after therapy), every 6 months for years 2 and 3, and annually for years 4 and 5. For pHGG we do MRI imaging every 3 months for year 1, every 4 months for year 2, every 6 months for years 3-5, and annually for years 6-10. It is uncertain if this imaging schedule is optimal in terms of tracking tumor evolution post-treatment. pLGG are a diverse group of tumors but generally tend have a slower progression rate when compared to pHGG. Studies have shown a 5-year progression-free survival (PFS) of 45% to 65% for residual tumor of any size for pLGG. 3-year PFS for pHGG at best is 18%. When possible, spacing imaging, decreasing sedations, and decreasing gadolinium-based contrast agents that can deposit in the body are key drivers in imaging schedules. Through retrospective analysis we are establishing if imaging schedules should be adjusted based on disease progression or recurrence.
DIPG-56. PEDIATRIC GLIOMAS EXHIBIT A UNIQUE LIPID METABOLIC PHENOTYPE DISTINCT FROM ADULT GBMS
Authors: Jennifer Salinas, Jenna Minami, Nicholas Bayley, Christopher Tse, Henan Zhu, Hong Tum, Timothy Cloughesy, Linda Liau, Thomas Graber, David Nathanson
Journal: Neuro-Oncology (2023)

Abstract Pediatric and adult IDH-wildtype gliomas (GBM) differ in both their clinical and molecular characteristics. However, whether distinct metabolic vulnerabilities exist between these two types of malignant brain tumors is unknown. Here, we performed integrated molecular and lipidomic profiling of both adult IDHwt and pediatric gliomas to identify distinguishable lipid phenotypes and consequent vulnerabilities. This analysis revealed IDHwt gliomas have heightened de novo lipid biosynthetic programs with an elevated abundance of triacylglycerides (TAGs). By contrast, pediatric gliomas exhibited lower lipid biosynthetic capacity and contained a higher enrichment for phospholipids. As a consequence of this unique metabolic program, pediatric gliomas relied of uptake of environmental complex fatty acids derived from normal resident brain cells for growth. Accordingly, therapeutic abrogation of lipid scavenging pathways selectively inhibited proliferation of pediatric gliomas compared to adult IDHwt counterparts. Together, these studies identify distinct metabolic programs among adult and pediatric gliomas, revealing new therapeutically actionable targets to slow pediatric glioma growth.
DIPG-39. SIGNALING NETWORKS IN PEDIATRIC-TYPE DIFFUSE HIGH GRADE GLIOMAS
Authors: Sophie A Herbst, Ryuhjin Ahn, Sameer Agnihotri, Michal Zapotocky, Forest M White
Journal: Neuro-Oncology (2023)

Abstract Pediatric-type diffuse high grade gliomas are aggressive brain cancers in children which to date lack effective treatment options and remain largely understudied. Even though genomic markers including histone H3 K27M and G34R mutations have been identified, their functional implications on signaling networks remain to be described. Phosphoproteomics might be able to uncover activated signaling pathways which could open up new paths for treatment. Here we analyzed formalin-fixed paraffin-embedded (FFPE) sections from K27M mutated, G34R mutated and histone H3 wild type patient tumors (n = 14) using phosphoproteomics. Our workflow not only enables the comprehensive characterization of phosphoserines and threonines but also of phosphotyrosines which, despite being rare modifications (0.1-1% of all phosphorylations), are known to play an important role in cancer. We found that signaling networks were distinct between the different tumor subtypes. For phosphotyrosines, tumor subtype accounted for the largest source of variation in the data (44% of variance) as determined by principle component analysis. The separation by subtype could also be seen from serine and threonine phosphoproteomics and proteomics, but was not as striking as for the phosphotyrosine data. Differential abundance analysis, partial least squares discriminant analysis and self-organizing maps revealed deregulated signaling networks between subtypes. The most downregulated pathway in K27M compared to wild type tumors was enriched for proteins involved in the epigenetic regulation of gene expression (FDR&amp;lt;5%), which is in accordance with the remodeling of the epigenome taking place in K27M mutated tumors. In addition, we could identify signaling networks (e.g. EGFR signaling) which were activated in a few individual patients independent of their subtype and might be targetable. Our study provides insights into the signaling landscape of pediatric-type diffuse high grade gliomas. Recognizing deregulated signaling networks across subtypes and in individual patients could offer new avenues for personalized therapy.